Stable isotope applications in biogeochemistry address many questions at the interface of geochemistry and biology such as those relating to pathways of carbon assimilation and degradation, nutrient cycling, and the environmental changes recorded in lipid biomarkers. My background is in organic and stable isotope geochemistry, as well as environmental microbiology. My past and present research focus is on the connection between microbial ecology, physiological responses to environmental change and the production of lipid biomarkers that may eventually become part of the geologic record. In particular, I have focused on hydrocarbon associated systems including coal beds and marine hydrocarbon cold seeps using a combination of stable isotope tracers, geochemical profiles and molecular biology to evaluate connections between the observed microbial ecology, geochemistry and breakdown of particular compounds.

I am currently working on developing techniques for the application of 33S and 34S labeled sulfate and elemental sulfur in probing biological sulfur cycling. Using environmental microbial communities from White Point Beach, CA, I examined the intracellular transfer of biologically derived sulfide with triple stable isotope labeling experiments: 13C, 15N and 33S or 34S. Silicon wafers colonized by microbial mats in situ, were incubated with isotopically labeled substrates and subsequently analyzed by fluorescent in situ hybridization (FISH) coupled to nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowing the simultaneous measurement of 13C/12C, 15N/14N, 33S/32S and 34S/32S of individual cells.

Cluster analysis of cells based on isotope ratio phenotypeIdentification of differences in carbon and sulfur metabolism in different cell types from an incubation with 33S-sulfate, 13C-acetate and 15N-ammonium. The 12C14N ion image (A) was used to determine regions of interest (ROI) (B). The ratios of C/N, S/N, 12C/13C, 15N/14N and 33S/32S were used in k-means cluster analysis (k=5) to determine groups of similar cell types amongst the ROIs (C). The various clusters show differences in 13C (D) and 33S (E) enrichment as well as cellular S content (F). The ROIs, after being colored by cluster and displayed based on position (G), correlate with cell types independently identified by fluorescent in situ hybridization (H and I).

The microbially mediated anaerobic oxidation of methane (AOM) is carried out by anaerobic methane-oxidizing archaea (ANME) in syntrophic association with sulfate-reducing bacteria (SRB). Understanding the metabolic interplay between the ANME and SRB in consortia is made difficult by the lack of cultured representatives. However, methanogenic archaea, that are closely related to their ANME counterparts, and SRB also form syntrophic consortia in both the environment and in laboratory grown co-cultures. Zhang et al. (2009, PNAS) demonstrated that the central metabolic pathway is reflected in the hydrogen isotopic fractionation between bacterial fatty acids and growth water. I am comparing the hydrogen isotopic fractionation of fatty acids from SRB cultures, aggregate forming archaeal and bacterial co-cultures and sediment cores associated with a variety of active methane seep settings. Syntrophic associations in these systems shift the δD of fatty acids from the values typically for selected growth conditions. This indicates that hydrogen is likely an important intermediate in these syntrophic systems and that mixed microbial communities in the environmental present an additional challenge to the application of this proxy for metabolic pathways requiring more study of mixed cultures

I studied microbial degradation of isoprenoid biomarkers in experiments using isotopically labeled lipids prepared from microbial cultures. In laboratory grown cultures, I enriched for denitrifying microorganisms capable of degrading acyclic isoprenoid analogues for archaeal diphytanyl glycerol diether (DGD) and glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids. In order to provide a stable isotopic tracer of isoprenoid degradation, I prepared 13C-labeled phytane from the core lipids of halophilic archaea that had incorporated a 13C-label into membrane lipids. ﻿Using the isotopically labeled tracer, I was able to definitively link microbes in culture to the degradation of phytane. Further, the presence of a stable isotope tracer in addition to concentrations of DIC, nitrate and nitrite enabled the prediction of a reaction stoichiometry and a degradation rate constant ﻿

A comparison of 454 tag pyrosequencing and quantitative fluorescent in situ hybridization (FISH) identified the active microbial community in gas field production waters from the Cook Inlet, Alaska. Microbial community composition in combination with methane isotope analysis indicated methane production by a methyl-type fermentation with two major genera of methanogenic Archaea, Methanosarcina and Methanolobus.

I am also interested in the relationship between
physiological responses to environmental conditions and membrane lipid
production in archaea. I examined the variation in the molecular structure of halophilic archaeal lipids grown at different salinities. This study identified unsaturated analogues of archaeol in four halophilic archaeal strains and revealed an increase in the percentage of unsaturated lipids with increasing salinity. Increasing membrane lipid unsaturation with increasing salt concentration suggests that unsaturation serves a role in maintaining the appropriate fluidity while reducing permeability in hypersaline condition.